Why is my turntable sounding so muddy?

another cause can be a buildup of gunk on the stylus. The big wads are easily seen but i have noticed a buildup can cause the sound to be muffled or muddled. A little Magic Eraser can remove that from being a source of the issue

Thanks for all the positive feedback. I tried a few things that you guys mentioned and the one thing I did was put the original cartridge back on.
It sounds better but still not quite what I think is correct? My next move is new tubes I will give that a try. Czarivey your thought is the one 
I thought about and that is why I went back to the original cartridge. I don't have the manual on my Counterpoint SA3 and looked on line for where the setting are but no luck yet. Again thanks for you help.

Could there be corrosion on any of the connections?  Maybe it's time to clean the contacts?

I'd run that preamp for a week before taking it seriously. Electronics don't like sitting around for years without being run. Audio equipment has a way of not sounding right when you turn it on again (or ever- unless it gets serviced out after not running for a while).

The phono section is arguably the most sensitive part of the preamp in more ways than one. Give it some time!

Could be as simple as a dirty stylus. Obviously be very gentle, use a tight pile stylus brush with the tonearm free and not locked down. Apply no more pressure than the tracking force, back to front. Hope this helps.